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- PDB-4jlx: Structure of porcine cyclic GMP-AMP synthase (cGAS) -

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Basic information

Entry
Database: PDB / ID: 4jlx
TitleStructure of porcine cyclic GMP-AMP synthase (cGAS)
ComponentsUncharacterized protein
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / cGAS/STING signaling pathway / negative regulation of double-strand break repair via homologous recombination / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cGMP-mediated signaling / cAMP-mediated signaling ...cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / cGAS/STING signaling pathway / negative regulation of double-strand break repair via homologous recombination / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cGMP-mediated signaling / cAMP-mediated signaling / nucleosome binding / positive regulation of type I interferon production / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / molecular condensate scaffold activity / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / defense response to virus / nuclear body / DNA repair / innate immune response / DNA damage response / chromatin binding / GTP binding / protein homodimerization activity / DNA binding / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21-like, nucleotidyltransferase domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / Beta Polymerase; domain 2 ...Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21-like, nucleotidyltransferase domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsCivril, F. / Hopfner, K.P.
CitationJournal: Nature / Year: 2013
Title: Structural mechanism of cytosolic DNA sensing by cGAS
Authors: Civril, F. / Deimling, T. / Mann, C.C.O. / Ablasser, A. / Moldt, M. / Witte, G. / Hornung, V. / Hopfner, K.P.
History
DepositionMar 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3248
Polymers42,4721
Non-polymers8527
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.402, 118.014, 142.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein


Mass: 42472.164 Da / Num. of mol.: 1 / Fragment: UNP residues 135-495
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MB21D1 / Production host: Escherichia coli (E. coli) / References: UniProt: I3LM39

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Non-polymers , 5 types, 133 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONFLICTS (ASP 268 AND THR 269) ARE DUE TO POLYMORPHISM AS IT IS NATURALLY OCCURRING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.61 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00665 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00665 Å / Relative weight: 1
ReflectionResolution: 2→47.5 Å / Num. obs: 51611

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.004→45.458 Å / SU ML: 0.22 / σ(F): 0.9 / Phase error: 22.93 / Stereochemistry target values: ML
Details: INITIAL MODEL IS SAD WHICH IS USED FOR MOLECULAR REPLACEMENT.
RfactorNum. reflection% reflection
Rfree0.2147 2578 5 %
Rwork0.188 --
obs0.1894 51611 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.004→45.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 54 126 3039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082991
X-RAY DIFFRACTIONf_angle_d1.0664006
X-RAY DIFFRACTIONf_dihedral_angle_d16.81159
X-RAY DIFFRACTIONf_chiral_restr0.076423
X-RAY DIFFRACTIONf_plane_restr0.004509
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.004-2.04220.29161350.2831257694
2.0422-2.08380.27871390.25682692100
2.0838-2.12920.28881440.2507274399
2.1292-2.17870.26461470.22342726100
2.1787-2.23320.27211420.22212747100
2.2332-2.29350.27251420.21992725100
2.2935-2.3610.27851500.21242770100
2.361-2.43720.22381420.21252721100
2.4372-2.52430.27611450.20462708100
2.5243-2.62540.27371440.20582762100
2.6254-2.74490.221410.20472712100
2.7449-2.88960.18161440.19222768100
2.8896-3.07060.2291430.18522696100
3.0706-3.30760.21131450.182759100
3.3076-3.64030.17991430.17212732100
3.6403-4.16680.17781430.1643271799
4.1668-5.24840.19351480.16222746100
5.2484-45.47020.20981410.18652733100

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